Variant report

Variant	rs4808962
Chromosome Location	chr19:19579557-19579558
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:27)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:27 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr19:19579401-19579562	K562	blood:	n/a	n/a
2	TCF12	chr19:19579166-19579704	A549	lung:	n/a	n/a
3	MAFF	chr19:19579350-19579561	HepG2	liver:	n/a	chr19:19579378-19579396
4	KAP1	chr19:19578795-19579787	HEK293	kidney:	n/a	n/a
5	POLR2A	chr19:19579269-19579944	K562	blood:	n/a	n/a
6	TRIM28	chr19:19579248-19579605	K562	blood:	n/a	n/a
7	IRF1	chr19:19579380-19579673	K562	blood:	n/a	n/a
8	ZNF143	chr19:19579260-19579639	GM12878	blood:	n/a	n/a
9	KAP1	chr19:19579118-19579743	U2OS	brain:	n/a	n/a
10	POLR2A	chr19:19579554-19579574	K562	blood:	n/a	n/a
11	USF1	chr19:19579249-19579586	SK-N-SH	brain:	n/a	n/a
12	KAP1	chr19:19578645-19579928	K562	blood:	n/a	n/a
13	MAFK	chr19:19579354-19579582	HepG2	liver:	n/a	chr19:19579379-19579394
14	ZNF143	chr19:19579280-19579594	H1-hESC	embryonic stem cell:	n/a	n/a
15	SETDB1	chr19:19578976-19579841	U2OS	brain:	n/a	n/a
16	ZNF143	chr19:19579253-19579587	Hela-S3	cervix:	n/a	n/a
17	CBX3	chr19:19579116-19579719	HCT-116	colon:	n/a	n/a
18	ZNF143	chr19:19579237-19579596	K562	blood:	n/a	n/a
19	SETDB1	chr19:19578773-19579819	K562	blood:	n/a	n/a
20	TRIM28	chr19:19579116-19579692	K562	blood:	n/a	n/a
21	CBX3	chr19:19579006-19579737	K562	blood:	n/a	n/a
22	USF1	chr19:19579223-19579657	HCT-116	colon:	n/a	n/a
23	CBX3	chr19:19579167-19579711	K562	blood:	n/a	n/a
24	TCF12	chr19:19579068-19579750	SK-N-SH	brain:	n/a	n/a
25	POLR2A	chr19:19579207-19579728	K562	blood:	n/a	n/a
26	TCF12	chr19:19579097-19579778	SK-N-SH	brain:	n/a	n/a
27	IRF1	chr19:19579311-19579715	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19516490..19519551-chr19:19577584..19579824,3	MCF-7	breast:
2	chr19:19577936..19580342-chr19:19585609..19587741,3	MCF-7	breast:
3	chr19:19570376..19575066-chr19:19577857..19582377,6	K562	blood:
4	chr19:19571463..19575965-chr19:19576361..19580794,6	K562	blood:
5	chr19:19578231..19580851-chr19:19582569..19585456,2	K562	blood:
6	chr19:19515118..19519487-chr19:19577388..19580917,4	K562	blood:
7	chr19:19579004..19580878-chr19:19585404..19588085,2	MCF-7	breast:

No data

Variant related genes	Relation type
GATAD2A	TF binding region
ENSG00000167491	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1036215	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10406278	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11085264	1.00[CEU][hapmap];0.95[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11555053	0.93[CEU][hapmap]
rs11668203	1.00[EUR][1000 genomes]
rs11669558	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11669730	0.93[CEU][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11670687	0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11670761	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11670775	1.00[CEU][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11670882	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs11671253	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1529745	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1560687	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16996127	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs17684164	1.00[CEU][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17751061	0.93[CEU][hapmap]
rs2010506	0.84[CEU][hapmap];0.89[YRI][hapmap]
rs2011503	1.00[CEU][hapmap];0.95[YRI][hapmap]
rs2060274	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2060275	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2860494	0.82[EUR][1000 genomes]
rs2905429	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2905433	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2905434	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2916070	1.00[CEU][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2916072	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2916075	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2965178	0.83[EUR][1000 genomes]
rs2965179	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2965181	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2965184	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2965186	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2965187	0.84[AFR][1000 genomes]
rs2965190	0.93[CEU][hapmap]
rs2965195	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2965201	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34487417	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34667451	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs45556231	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs45631651	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4808204	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4808205	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4808206	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4808951	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4808958	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4808968	1.00[CEU][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4808969	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4808970	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55927782	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56280531	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56291054	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56330647	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58074958	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61744761	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6511027	0.93[CEU][hapmap]
rs6511029	0.81[EUR][1000 genomes]
rs7245689	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7250233	1.00[CEU][hapmap];0.90[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7252453	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs7256028	0.90[EUR][1000 genomes]
rs751857	0.95[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs754256	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs756997	1.00[CEU][hapmap];0.90[YRI][hapmap];0.83[EUR][1000 genomes]
rs8100927	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8101219	0.84[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8102502	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs8103992	0.80[CEU][hapmap]
rs8105642	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8110171	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8110250	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8111093	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4808962	SF4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19575600-19581600	ZNF genes & repeats	GM12878-XiMat	blood
2	chr19:19575800-19579600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr19:19575800-19579800	ZNF genes & repeats	Dnd41	blood
4	chr19:19575800-19580000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr19:19575800-19580600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
6	chr19:19575800-19580800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr19:19575800-19581600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:19576000-19579800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr19:19576200-19579600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr19:19576200-19580000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr19:19576200-19580200	ZNF genes & repeats	Thymus	Thymus
12	chr19:19576200-19580600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr19:19576200-19580800	ZNF genes & repeats	Primary B cells from cord blood	blood
14	chr19:19576400-19580000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr19:19576400-19580600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
16	chr19:19576400-19580600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
17	chr19:19576400-19580600	ZNF genes & repeats	Fetal Thymus	thymus
18	chr19:19576600-19580600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr19:19576600-19580800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr19:19576800-19579800	ZNF genes & repeats	K562	blood
21	chr19:19576800-19579800	ZNF genes & repeats	NHDF-Ad	bronchial
22	chr19:19576800-19580800	ZNF genes & repeats	Fetal Intestine Small	intestine
23	chr19:19577000-19579800	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
24	chr19:19577000-19579800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
25	chr19:19577000-19580000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr19:19577000-19580400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
27	chr19:19577200-19580200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr19:19577200-19580200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
29	chr19:19577200-19580200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr19:19577200-19580600	ZNF genes & repeats	Fetal Stomach	stomach
31	chr19:19577400-19579800	ZNF genes & repeats	Primary T cells from cord blood	blood
32	chr19:19577400-19579800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr19:19577400-19579800	ZNF genes & repeats	Brain Germinal Matrix	brain
34	chr19:19577400-19580400	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr19:19577400-19580600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
36	chr19:19577600-19579800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
37	chr19:19577600-19579800	ZNF genes & repeats	Brain Hippocampus Middle	brain
38	chr19:19577600-19579800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
39	chr19:19577600-19579800	ZNF genes & repeats	A549	lung
40	chr19:19577600-19579800	ZNF genes & repeats	HMEC	breast
41	chr19:19577600-19579800	ZNF genes & repeats	NHLF	lung
42	chr19:19577600-19580000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
43	chr19:19577600-19580000	ZNF genes & repeats	Fetal Muscle Trunk	muscle
44	chr19:19577600-19580400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
45	chr19:19577600-19580600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
46	chr19:19577600-19580600	ZNF genes & repeats	Fetal Lung	lung
47	chr19:19577600-19580600	ZNF genes & repeats	Fetal Muscle Leg	muscle
48	chr19:19577600-19580600	ZNF genes & repeats	HSMM	muscle
49	chr19:19577800-19580200	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
50	chr19:19577800-19580600	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum

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